ArrayTools

This package is for version 3.6 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ArrayTools.

geneChip Analysis Package

DOI: 10.18129/B9.bioc.ArrayTools

Bioconductor version: 3.6

This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

Author: Xiwei Wu, Arthur Li

Maintainer: Arthur Li <xueli at coh.org>

Citation (from within R, enter citation("ArrayTools")):

Installation

To install this package, start R (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("ArrayTools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ArrayTools")

1. Primer PDF R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, StatisticalMethod, Visualization

Version 1.38.0

In Bioconductor since BioC 2.3 (R-2.8) (15.5 years)

License LGPL (>= 2.0)

Depends R (>= 2.7.0), affy(>= 1.23.4), Biobase(>= 2.5.5), methods

Imports affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable

System Requirements

URL

Suggests simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ArrayTools_1.38.0.tar.gz

Windows Binary ArrayTools_1.38.0.zip

Mac OS X 10.11 (El Capitan) ArrayTools_1.38.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/ArrayTools

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ArrayTools

Package Short Url https://bioconductor.org/packages/ArrayTools/

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Old Source Packages for BioC 3.6 Source Archive